[gmx-users] FeS4 cluster

[David]

On Sat, 2002-12-07 at 13:03, Weihua Li wrote:
> >>  Here's a sample:
> >>  
> >>  5
> >>  CYS     SG      1       CYS     SG      1       0.2     CYS2    CYS2
> >>  
> >>  You want to add
> >>  Cys SG 1 FE FE 4 0.2 CYS1 FE
> >>   What is the meaning of 4?
> 
> that the FE can make 4 bonds.
>      What about the case in the HEME Fe and S of Cys? 5,or 2?
>   The value is 2 in the specbond.dat file.i don't know why? As you said,the value shoud be 5.

Chec your biochemistry textbook. There are different hemes around, the
iron has usually four bonds to nitrogens (these are not counted here
beacuse they are in the rtp file and should always be present in a
heme), but can have one or two to other ligands too.


-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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